Metalloproteinases in Restorative Dentistry: An In Silico Study Toward an Ideal Animal Model

Overview

Journal Biomedicines

Specialty Biomedical Engineering

Date 2023 Nov 25

PMID 38002041

Authors

Simone Gomes de Oliveira

Nelson Kotowski

Helio Rodrigues Sampaio-Filho

Flavio Henrique Baggio Aguiar

Alberto Martin Rivera Davila

Rodrigo Jardim

Affiliations

Soon will be listed here.

Abstract

In dentistry, various animal models are used to evaluate adhesive systems, dental caries and periodontal diseases. Metalloproteinases (MMPs) are enzymes that degrade collagen in the dentin matrix and are categorized in over 20 different classes. Collagenases and gelatinases are intrinsic constituents of the human dentin organic matrix fibrillar network and are the most abundant MMPs in this tissue. Understanding such enzymes' action on dentin is important in the development of approaches that could reduce dentin degradation and provide restorative procedures with extended longevity. This in silico study is based on dentistry's most used animal models and intends to search for the most suitable, evolutionarily close to . We were able to retrieve 176,077 mammalian MMP sequences from the UniProt database. These sequences were manually curated through a three-step process. After such, the remaining 3178 sequences were aligned in a multifasta file and phylogenetically reconstructed using the maximum likelihood method. Our study inferred that the animal models most evolutionarily related to were (MMP-1 and MMP-8), (MMP-13), (MMP-2) and (MMP-9). Further research will be needed for the biological validation of our findings.

References

Carvalho M, Leijoto-Lannes A, Rodrigues M, Nogueira L, Ferraz N, Moreira A . Viability of Bovine Teeth as a Substrate in Bond Strength Tests: A Systematic Review and Meta-analysis. J Adhes Dent. 2018; 20(6):471-479. DOI: 10.3290/j.jad.a41636. View

Chang A, Lin R, Keith Studley W, Tran C, Saier Jr M . Phylogeny as a guide to structure and function of membrane transport proteins. Mol Membr Biol. 2004; 21(3):171-81. DOI: 10.1080/09687680410001720830. View

Cui N, Hu M, Khalil R . Biochemical and Biological Attributes of Matrix Metalloproteinases. Prog Mol Biol Transl Sci. 2017; 147:1-73. PMC: 5430303. DOI: 10.1016/bs.pmbts.2017.02.005. View

Subbaraj G, Elangovan H, Chandramouli P, Yasam S, Chandrasekaran K, Kulanthaivel L . Antiangiogenic Potential of Troxerutin and Chitosan Loaded Troxerutin on Chorioallantoic Membrane Model. Biomed Res Int. 2023; 2023:5956154. PMC: 10229255. DOI: 10.1155/2023/5956154. View

Zhang H, Sun C, He B, Zhang X, Hao H, Hou Y . Macrophage Migration Inhibitory Factor Promotes Expression of Matrix Metalloproteinases 1 and 3 in Spinal Cord Astrocytes following Gecko Tail Amputation. J Integr Neurosci. 2023; 22(2):29. DOI: 10.31083/j.jin2202029. View

Checchi V, Maravic T, Bellini P, Generali L, Consolo U, Breschi L . The Role of Matrix Metalloproteinases in Periodontal Disease. Int J Environ Res Public Health. 2020; 17(14). PMC: 7399864. DOI: 10.3390/ijerph17144923. View

Letunic I, Bork P . Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021; 49(W1):W293-W296. PMC: 8265157. DOI: 10.1093/nar/gkab301. View

Harrison M, Abu-Elmagd M, Grocott T, Yates C, Gavrilovic J, Wheeler G . Matrix metalloproteinase genes in Xenopus development. Dev Dyn. 2004; 231(1):214-20. DOI: 10.1002/dvdy.20113. View

Chen Q, Britto R, Erill I, Jeffery C, Liberzon A, Magrane M . Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genomics Proteomics Bioinformatics. 2020; 18(2):91-103. PMC: 7646089. DOI: 10.1016/j.gpb.2018.11.006. View

10.

Wang S, Liu Y, Fang D, Shi S . The miniature pig: a useful large animal model for dental and orofacial research. Oral Dis. 2007; 13(6):530-7. DOI: 10.1111/j.1601-0825.2006.01337.x. View

11.

Price M, Dehal P, Arkin A . FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010; 5(3):e9490. PMC: 2835736. DOI: 10.1371/journal.pone.0009490. View

12.

Tang H, Finn R, Thomas P . TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Bioinformatics. 2018; 35(3):518-520. PMC: 6361231. DOI: 10.1093/bioinformatics/bty625. View

13.

Turk B, Lee D, Yamakoshi Y, Klingenhoff A, Reichenberger E, Wright J . MMP-20 is predominately a tooth-specific enzyme with a deep catalytic pocket that hydrolyzes type V collagen. Biochemistry. 2006; 45(12):3863-74. PMC: 2536712. DOI: 10.1021/bi052252o. View

14.

Ancuta D, Alexandru D, Crivineanu M, Coman C . Induction of Periodontitis Using Bacterial Strains Isolated from the Human Oral Microbiome in an Experimental Rat Model. Biomedicines. 2023; 11(8). PMC: 10452127. DOI: 10.3390/biomedicines11082098. View

15.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K . BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10:421. PMC: 2803857. DOI: 10.1186/1471-2105-10-421. View

16.

Mazzoni A, Mannello F, Tay F, Tonti G, Papa S, Mazzotti G . Zymographic analysis and characterization of MMP-2 and -9 forms in human sound dentin. J Dent Res. 2007; 86(5):436-40. DOI: 10.1177/154405910708600509. View

17.

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

18.

Mieliauskaite D, Kontenis V, Siaurys A . Lessons from Animal Models in Sjögren's Syndrome. Int J Mol Sci. 2023; 24(16). PMC: 10454747. DOI: 10.3390/ijms241612995. View

19.

Gimenes S, Sachett J, Colombini M, Freitas-de-Sousa L, Ibiapina H, Costa A . Observation of Snake Envenoming Blister Formation from Five Patients: Pathophysiological Insights. Toxins (Basel). 2021; 13(11). PMC: 8618272. DOI: 10.3390/toxins13110800. View

20.

Assuncao Vialle R, Tamuri A, Goldman N . Alignment Modulates Ancestral Sequence Reconstruction Accuracy. Mol Biol Evol. 2018; 35(7):1783-1797. PMC: 5995191. DOI: 10.1093/molbev/msy055. View